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Aboard the UNSC Red Horse close to the wreckage of Alpha Halo, a team of Marines and naval personnel led by SergeantLopez recovers an escape pod from the Mona Lisa. Inside the pod is a critically injured man who says little but to express his relief at being safe before expiring. Sergeant Lopez is summoned to meet with the CO of the Red Horse, Captain Foucault, and the new AI, Rebecca. Lopez is ordered to take her team and investigate the Mona Lisa, although exactly what she is supposed to be looking for is left unclear. Lopez realizes that her team consists of everyone who has come into contact with the John Doe inside the escape pod. These include Ngoc Benti, a corpsman, Clarence, an extremely competent and quiet private, MacCraw, the loud and experienced rookie in their squad, and Burgundy, a crack Pelican pilot.

Lopez's squad boards the drifting Mona Lisa and quickly cleans up a small group of unarmed, unarmored Covenant Elites. Benti, chasing a Covenant Elite, runs almost directly into it. The Elite, to Benti's surprise, puts its finger to its mouth in a "shush" gesture. Benti hesitates, and the Elite is gunned down by Clarence. After they finish killing the few Covenant in the area, one of the Marines goes missing. Lopez assigns a small group of Marines to stay behind and guard the Pelican while the rest look for their missing squadmate. The lost Marine, nicknamed Rabbit, is soon found dead with another unarmed Elite repeatedly stomping on her chest. While removing Rabbit's dog tags, Lopez notices unnatural growth on the body. At the same time, the Marines left to guard the Pelican engage an unseen enemy, and are quickly overrun. Burgundy stays inside the Pelican and watches as their bodies disappear.

The remaining Marines make contact with Foucault, who orders them to initiate the Cole Protocol, seeing as there are loose Covenant on the ship, and erase the ship's nav data. Lopez divides up her remaining men into two groups, one led by herself to destroy the nav data in the bridge and the other led by Benti to destroy the backup in the engine room. As Benti's team leaves, Lopez realizes that another Marine, Ayad, is also mysteriously missing.

Lopez and her squad make their way to the ship's minimal medical bay, there they find a sealed safe room, and it opens to reveal the ship's supposed medical officer, John Smith. After encountering a strange growth within the ship, Lopez verbally interrogates Smith, who reluctantly reveals that experiments were being conducted on Covenant prisoners with an unknown infection, but then the infection jumped to the human prisoners aboard the ship. Burgundy sees a few of the Marines outside, badly wounded but apparently still alive, and opens the Pelican for them to get in. Up close, Burgundy realizes that the Marines are in fact dead and deformed, yet are still walking, and attempts to stop them from getting too her. She is overpowered and dragged away. Benti's group makes its way into the bilges of the ship but is soon engaged by a group of the Flood. As the Marines make their escape, one of their number is wounded, expires and later wakes up to bite another Marine. Lopez loses another man to the Flood, and eventually finds that Smith is actually an ONI operative. Smith breaks free from Lopez and makes it back to the Red Horse in the Marine's Pelican. Benti finds a human survivor, Rimmer, and a befriended Elite armed with a cricket bat, "Henry".

Rimmer points out that one of Benti's party is infected. The infected Marine is promptly shot in the head by Clarence, reanimates and is shot again. During an engagement with an infected Elite, Lopez's group loses two more Marines, leaving only herself and MacCraw. Lopez makes contact with the Red Horse one last time, and she is informed that Foucault will destroy the Mona Lisa to ensure that the Flood do not escape. Benti's team, now only consisting of herself, Clarence, Rimmer and "Henry", finally reaches the engine room and witnesses Burgundy being dragged to a huge growth on the engine. Realizing that the Flood are trying to "hot wire" the Slipspace drive to work, Benti throws her last grenades at the Flood growth to destroy it, and begins to fall back.

They meet up with Lopez and MacCraw outside the airlock for the escape pods, but Benti is injured by an infected Marine. When Lopez sees "Henry" and Rimmer, Clarence shoots Rimmer in the head and is revealed to also be an ONI agent. As the survivors standoff, MacCraw takes one of the two remaining escape pods and abandons them. The wounded Benti manages to push Clarence into the army of Flood pursuing them, and both of them are taken. Lopez and "Henry" hold off the Flood long enough to enter the airlock, but then they realize that there is only enough room for one in the remaining escape pod. Lopez tries to shoot "Henry", but realizes she is out of ammunition. The two begin fighting for the last pod as the countdown timer to Foucault's attack reaches thirty seconds.

When writing the story, Tessa Kum and Jeff VanderMeer used Halo Nation for some of the in-universe details, due to the fact they were not given the official Halo Story Bible.[2] Due to this, there are a small number of details found in the story that aren't found in the games, such as the Flood's ability to infect an organism by simply wounding them, which causes them to mutate without an initial infection form present.

In the motion comic adaptation, Threshold is erroneously depicted as being blue. In original Halo canon, the planet is a rusty orange.[1]

The animated short bears a striking resemblance to Dead Space: Downfall, another "space zombie" horror story based on its respective video game series.

The motion comic adaptation drops a number of characters from the story, including Ayad, Maller, Simmons, Sydney, Percy and Rakesh. It also makes no mention of the Red Horse's former A.I. Chauncey, and does not show nor mention Rebecca's alternate avatar of a Mediterranean woman.

The motion comic removes a number of themes, such as Lopez viewing her squad as her "rosary beads" after a single mention, and rewrites the unknown injured man into dying moments after he is removed from the pod, rather than in the medical ward of the Red Horse. This was presumably to cut down on time.

There is a mistake on page 261 of the original version: "Thought Benti, with Clarence, would be more effective heading things up on that team than Orlav." Thought should be though.